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- PDB-1yu0: Major Tropism Determinant P1 Variant -

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Basic information

Entry
Database: PDB / ID: 1yu0
TitleMajor Tropism Determinant P1 Variant
ComponentsMajor Tropism Determinant (Mtd-P1)
KeywordsVIRAL PROTEIN / C-type Lectin / Beta Sandwich / Beta Prism / variability / diversity-generating retroelement
Function / homology
Function and homology information


viral tropism switching / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily / Seminal Fluid Protein PDC-109 (Domain B) / C-type lectin fold ...Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily / Seminal Fluid Protein PDC-109 (Domain B) / C-type lectin fold / Trefoil / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tail fiber receptor-binding protein
Similarity search - Component
Biological speciesBordetella phage BPP-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å
AuthorsMcMahon, S.A. / Miller, J.L. / Lawton, J.A. / Ghosh, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The C-type lectin fold as an evolutionary solution for massive sequence variation
Authors: McMahon, S.A. / Miller, J.L. / Lawton, J.A. / Kerkow, D.E. / Hodes, A. / Marti-Renom, M.A. / Doulatov, S. / Narayanan, E. / Sali, A. / Miller, J.F. / Ghosh, P.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major Tropism Determinant (Mtd-P1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6383
Polymers39,5571
Non-polymers802
Water8,791488
1
A: Major Tropism Determinant (Mtd-P1)
hetero molecules

A: Major Tropism Determinant (Mtd-P1)
hetero molecules

A: Major Tropism Determinant (Mtd-P1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9139
Polymers118,6723
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area14230 Å2
ΔGint-111 kcal/mol
Surface area35100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.258, 92.258, 102.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-501-

CA

21A-502-

CA

31A-758-

HOH

41A-862-

HOH

51A-932-

HOH

DetailsThe biological assembly is a trimer generated from: -y, x-y, z and -x+y, -x, z

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Components

#1: Protein Major Tropism Determinant (Mtd-P1)


Mass: 39557.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella phage BPP-1 (virus) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q775D6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 550 MME, HEPES, calcium chloride, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.1055
SYNCHROTRONAPS 19-ID20.97910, 0.97932, 0.95372
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.10551
20.97911
30.979321
40.953721
ReflectionResolution: 1.56→50 Å / Num. all: 69212 / Num. obs: 69212 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.56→1.62 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.56→20.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.693 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14478 3496 5.1 %RANDOM
Rwork0.12755 ---
all0.12843 69212 --
obs0.12843 69212 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.629 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 2 488 3248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212828
X-RAY DIFFRACTIONr_bond_other_d0.0010.022430
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9073856
X-RAY DIFFRACTIONr_angle_other_deg0.76535620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58923.534116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.36315378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1691512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
X-RAY DIFFRACTIONr_nbd_refined0.2060.2516
X-RAY DIFFRACTIONr_nbd_other0.1870.22361
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21459
X-RAY DIFFRACTIONr_nbtor_other0.0840.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2290
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.250
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1150.28
X-RAY DIFFRACTIONr_mcbond_it0.6891.51870
X-RAY DIFFRACTIONr_mcbond_other0.1561.5792
X-RAY DIFFRACTIONr_mcangle_it1.08122915
X-RAY DIFFRACTIONr_scbond_it1.79131115
X-RAY DIFFRACTIONr_scangle_it2.4474.5941
LS refinement shellResolution: 1.56→1.599 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.163 274 -
Rwork0.127 4856 -
obs--99 %

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